I would change the other routine, but anyway, a simple solution would be double quote all the fields regardless.

#!perl
use strict;
open OUT,">test.csv" or die "$!";

while (<DATA>){
  chomp;
  s/;;/","/g;
  print OUT '"'.$_.'"'."\n";
}
close OUT;

__DATA__
abd;;sasa;;trre,dsa;;sdas;;dsss
abd;;sasa;;trre,dsa;;sdas;;dsss
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poj